/MoSDeF-workshop

Collection of tutorials and example workflows for MoSDeF workshop at FOMMS 2022

Primary LanguageJupyter NotebookMIT LicenseMIT

MoSDeF - The Molecular Simulation Design Framework

The Molecular Simulation and Design Framework (MoSDeF) is a collection of open-source tools (hosted on Github) aims at facilitating the construction and simulation of complex molecular systems - with a particular focus on the automated screening of large structural parameter spaces. All tools are written as Python packages and feature a Python-based API.

The MoSDeF software suite consist of three core libraries, namely mBuild, Foyer, and GMSO. Each library dedicates to handle a certain step of the chemical system initialization process, as summarized in the figure below.

MoSDeF Ecosystem

Libraries in the MoSDeF ecosystem are designed to provide utilities necessary to streamline a researcher's simulation workflow. When setting up simulation studies, we also recommend users to follow the TRUE (Transparent, Reproducible, Usable-by-others, and Extensible) standard, which is a set of common practices meant to improve the reproducibility of computational simulation research.

This Workshop

Due to time constraint, this workshop could not cover all the details and features that offers by the MoSDeF tools. However, we will visit several key data structures and features that would allow new users to quickly onboard and start using MoSDeF on their research. Together, we will walk through a set of tutorials, focus on individual tools in the software suite, namely mBuild, Foyer and GMSO. These tutorials will be presented in a series of Jupyter notebook, which participants can choose to download and fire up these notebooks locally or access it through Mybinder. If you choose to download the tutorials and host them locally, please follow the installation instruction below. Please leave your comment question during this workshop to the etherpad link: https://etherpad.boisestate.edu/p/mosdef-fomms2022

Installation

Follow the command below to clone and create the conda environment for this repository. Assuming you already have conda installed locally:

conda install mamba -n base -c conda-forge

git clone https://github.com/mosdef-hub/fomms-workshop.git
cd fomms-workshop

mamba env create -f environment.yml
mamba activate mosdef-workshop

jupyter notebook

Mybinder Binder

Follow the image above to test this repository through the Mybinder service, or follow this link: https://mybinder.org/v2/gh/mosdef-hub/FOMMS-workshop/HEAD

Additional Resources

More in-depth MoSDeF tutorials: https://github.com/mosdef-hub/mosdef_tutorials

Example MoSDeF workflow: https://github.com/mosdef-hub/mosdef-workflows

Documentations:

Join our mailing list: https://groups.google.com/g/mosdef-users

FOMMS Logo         MoSDeF Logo